I have a dvb card with two inputs connected to two different satellites. Is it possible to record both of the chans on these inputs at once with progdvb? If so, how can this be done?

Yes. Possible. You can simple open second channel when you record first. Or use context menu or PIP functions.

Progdvb crashes when I try enabling 2 tuners in the options. Is it possible to run 2 installs of probdvb and have 1 tuner selected on each install? With other dvb apps I'm able to copy the install directory to another location and then run 2 copies of the app. Not sure prog can do the same as it looks like it has some folders outside of the install directory in c:\users\user\app data\local\progdvb.

You can enable both tuners in ProgDVB.